| Type: | Package |
| Title: | Tools for Pre-Processing Emission-Excitation-Matrix (EEM) Fluorescence Data |
| Version: | 1.0.2 |
| Description: | Provides various tools for preprocessing Emission-Excitation-Matrix (EEM) for Parallel Factor Analysis (PARAFAC). Different methods are also provided to calculate common metrics such as humification index and fluorescence index. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| BugReports: | https://github.com/PMassicotte/eemR/issues |
| URL: | https://github.com/PMassicotte/eemR |
| Depends: | R (≥ 3.2.1) |
| LazyData: | TRUE |
| Imports: | stringr, dplyr, R.matlab, pracma, stats, rlist, viridis, purrr, assertthat |
| RoxygenNote: | 7.3.2 |
| Suggests: | cdom, magrittr, testthat (≥ 2.1.0), knitr, rmarkdown, ggplot2, plot3D, extrafont, tidyr, shiny, DT, MBA, here, covr |
| VignetteBuilder: | knitr |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| Packaged: | 2025-03-24 13:21:44 UTC; filoche |
| Author: | Philippe Massicotte [aut, cre] |
| Maintainer: | Philippe Massicotte <pmassicotte@hotmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-03-24 14:40:11 UTC |
eemR: Tools for Pre-Processing Emission-Excitation-Matrix (EEM) Fluorescence Data
Description
Provides various tools for preprocessing Emission-Excitation-Matrix (EEM) for Parallel Factor Analysis (PARAFAC). Different methods are also provided to calculate common metrics such as humification index and fluorescence index.
Author(s)
Maintainer: Philippe Massicotte pmassicotte@hotmail.com
See Also
Useful links:
CDOM absorbance data.
Description
Simple absorbance spectra used to test package's functions.
Usage
data("absorbance")
Format
A data frame with 711 rows and 4 variables
Details
wavelength. Wavelengths used for measurements (190-900 nm.)
absorbance
Examples
data("absorbance")
plot(absorbance$wavelength, absorbance$sample1,
type = "l",
xlab = "Wavelengths", ylab = "Absorbance per meter"
)
lines(absorbance$wavelength, absorbance$sample2, col = "blue")
lines(absorbance$wavelength, absorbance$sample3, col = "red")
eem constructor
Description
eem constructor
Usage
eem(data)
Arguments
data |
A list containing "file", "x", "em", "ex". |
Value
An object of class eem containing:
sample The sample name of the eem.
file The filename of the eem.
location Directory of the eem.
x A matrix with fluorescence values.
em Emission vector of wavelengths.
ex Excitation vector of wavelengths.
Bind eem or eemlist
Description
Function to bind EEMs that have been loaded from different folders or have been processed differently.
Usage
eem_bind(...)
Arguments
... |
One or more object of class |
Value
An object of eemlist.
Examples
file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
eem <- eem_read(file, import_function = "cary")
eem <- eem_bind(eem, eem)
Calculate the biological fluorescence index (BIX)
Description
The biological fluorescence index (BIX) is calculated by dividing the fluorescence at excitation 310 nm and emission at 380 nm (ex = 310, em = 380) by that at excitation 310 nm and emission at 430 nm (ex = 310, em = 430).
Usage
eem_biological_index(eem, verbose = TRUE)
Arguments
eem |
An object of class |
verbose |
Logical determining if additional messages should be printed. |
Value
An object of class eemlist.
A data frame containing the biological index (BIX) for each eem.
Interpolation
Different excitation and emission wavelengths are often used to measure
EEMs. Hence, it is possible to have mismatchs between measured wavelengths
and wavelengths used to calculate specific metrics. In these
circumstances, EEMs are interpolated using the
interp2 function from the parcma library. A
message warning the user will be prompted if data interpolation is
performed.
References
Huguet, A., Vacher, L., Relexans, S., Saubusse, S., Froidefond, J. M., & Parlanti, E. (2009). Properties of fluorescent dissolved organic matter in the Gironde Estuary. Organic Geochemistry, 40(6), 706-719.
doi:10.1016/j.orggeochem.2009.03.002
See Also
Examples
file <- system.file("extdata/cary/scans_day_1/", package = "eemR")
eem <- eem_read(file, import_function = "cary")
eem_biological_index(eem)
Extract fluorescence peaks
Description
Extract fluorescence peaks
Usage
eem_coble_peaks(eem, verbose = TRUE)
Arguments
eem |
An object of class |
verbose |
Logical determining if additional messages should be printed. |
Details
According to Coble (1996), peaks are defined as follow:
Peak B: ex = 275 nm, em = 310 nm
Peak T: ex = 275 nm, em = 340 nm
Peak A: ex = 260 nm, em = 380:460 nm
Peak M: ex = 312 nm, em = 380:420 nm
peak C: ex = 350 nm, em = 420:480 nm
Given that peaks A, M and C are not defined at fix emission wavelength, the maximum fluorescence value in the region is extracted.
Value
An object of class eemlist.
A data frame containing peaks B, T, A, M and C for each eem. See details for more information.
Interpolation
Different excitation and emission wavelengths are often used to measure
EEMs. Hence, it is possible to have mismatchs between measured wavelengths
and wavelengths used to calculate specific metrics. In these
circumstances, EEMs are interpolated using the
interp2 function from the parcma library. A
message warning the user will be prompted if data interpolation is
performed.
References
Coble, P. G. (1996). Characterization of marine and terrestrial DOM in seawater using excitation-emission matrix spectroscopy. Marine Chemistry, 51(4), 325-346.
doi:10.1016/0304-4203(95)00062-3
See Also
Examples
file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
eem <- eem_read(file, import_function = "cary")
eem_coble_peaks(eem)
Cut emission and/or excitation wavelengths from EEMs
Description
Cut emission and/or excitation wavelengths from EEMs
Usage
eem_cut(eem, ex, em, exact = TRUE, fill_with_na = FALSE)
Arguments
eem |
An object of class |
ex |
A numeric vector of excitation wavelengths to be removed. |
em |
A numeric vector of emission wavelengths to be removed. |
exact |
Logical. If TRUE, only wavelengths matching |
fill_with_na |
Logical. If TRUE, fluorescence values at specified wavelengths will be replaced with NA. If FALSE, these values will be removed. |
Value
An object of class eemlist.
Examples
# Open the fluorescence eem
file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
eem <- eem_read(file, import_function = "cary")
plot(eem)
# Cut few excitation wavelengths
eem <- eem_cut(eem, ex = c(220, 225, 230, 230))
plot(eem)
eem <- eem_read(file, import_function = "cary")
eem <- eem_cut(eem, em = 350:400, fill_with_na = TRUE)
plot(eem)
Export EEMs to Matlab
Description
Export EEMs to Matlab
Usage
eem_export_matlab(file, ...)
Arguments
file |
The .mat file name where to export the structure. |
... |
One or more object of class |
Details
The function exports EEMs into PARAFAC-ready Matlab .mat file
usable by the drEEM toolbox.
Value
A structure named OriginalData is created and contains:
- nSample
The number of eems.
- nEx
The number of excitation wavelengths.
- nEm
The number of emission wavelengths.
- Ex
A vector containing excitation wavelengths.
- Em
A vector containing emission wavelengths.
- X
A 3D matrix (nSample X nEx X nEm) containing EEMs.
sample_name The list of sample names (i.e. file names) of the
imported EEMs.
Known bug in export
eemR uses R.Matlab to export the
the fluorescence data into a matfile. However, there is currently a bug in
the latter package that require the user to reshape the exported data once
in Matlab. This can be done using the following command:
load('OriginalData.mat'); OriginalData.X = reshape(OriginalData.X,
OriginalData.nSample, OriginalData.nEm, OriginalData.nEx)
Examples
file <- system.file("extdata/cary/", package = "eemR")
eem <- eem_read(file, recursive = TRUE, import_function = "cary")
export_to <- paste(tempfile(), ".mat", sep = "")
eem_export_matlab(export_to, eem)
Extract EEM samples
Description
Extract EEM samples
Usage
eem_extract(eem, sample, keep = FALSE, ignore_case = FALSE, verbose = TRUE)
Arguments
eem |
An object of class |
sample |
Either numeric of character vector. See |
keep |
logical. If TRUE, the specified |
ignore_case |
Logical, should sample name case should be ignored (TRUE) or not (FALSE). Default is FALSE. |
verbose |
Logical determining if removed/extracted eems should be printed on screen. |
Details
sample argument can be either numeric or character vector. If
it is numeric, samples at specified index will be removed.
If sample is character, regular expression will be used and all
sample names that have a partial or complete match with the expression will
be removed. See examples for more details.
Value
An object of class eemlist.
Examples
folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
eems <- eem_read(folder, import_function = "cary")
eems
# Remove first and third samples
eem_extract(eems, c(1, 3))
# Remove everything except first and third samples
eem_extract(eems, c(1, 3), keep = TRUE)
# Remove all samples containing "3" in their names.
eem_extract(eems, "3")
# Remove all samples containing either character "s" or character "2" in their names.
eem_extract(eems, c("s", "2"))
# Remove all samples containing "blank" or "nano"
eem_extract(eems, c("blank", "nano"))
Extract blank EEM
Description
Extract blank EEM
Usage
eem_extract_blank(eem, average = TRUE)
Arguments
eem |
An object of class |
average |
Logical. If TRUE blank EEMs will be averaged |
Value
An object of class eemlist.
Calculate the fluorescence index (FI)
Description
Calculate the fluorescence index (FI)
Usage
eem_fluorescence_index(eem, verbose = TRUE)
Arguments
eem |
An object of class |
verbose |
Logical determining if additional messages should be printed. |
Value
An object of class eemlist.
A data frame containing fluorescence index (FI) for each eem.
Interpolation
Different excitation and emission wavelengths are often used to measure
EEMs. Hence, it is possible to have mismatchs between measured wavelengths
and wavelengths used to calculate specific metrics. In these
circumstances, EEMs are interpolated using the
interp2 function from the parcma library. A
message warning the user will be prompted if data interpolation is
performed.
References
See Also
Examples
file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
eem <- eem_read(file, import_function = "cary")
eem_fluorescence_index(eem)
Calculate the fluorescence humification index (HIX)
Description
The fluorescence humification index (HIX), which compares two broad aromatic dominated fluorescence maxima, is calculated at 254 nm excitation by dividing the sum of fluorescence intensities between emission 435 to 480 nm by the the sum of fluorescence intensities between 300 to 345 nm.
Usage
eem_humification_index(eem, scale = FALSE, verbose = TRUE)
Arguments
eem |
An object of class |
scale |
Logical indicating if HIX should be scaled, default is FALSE. See details for more information. |
verbose |
Logical determining if additional messages should be printed. |
Value
An object of class eemlist.
A data frame containing the humification index (HIX) for each eem.
Interpolation
Different excitation and emission wavelengths are often used to measure
EEMs. Hence, it is possible to have mismatchs between measured wavelengths
and wavelengths used to calculate specific metrics. In these
circumstances, EEMs are interpolated using the
interp2 function from the parcma library. A
message warning the user will be prompted if data interpolation is
performed.
References
Ohno, T. (2002). Fluorescence Inner-Filtering Correction for Determining the Humification Index of Dissolved Organic Matter. Environmental Science & Technology, 36(4), 742-746.
See Also
Examples
file <- system.file("extdata/cary/scans_day_1/", package = "eemR")
eem <- eem_read(file, import_function = "cary")
eem_humification_index(eem)
Inner-filter effect correction
Description
Inner-filter effect correction
Usage
eem_inner_filter_effect(eem, absorbance, pathlength = 1)
Arguments
eem |
An object of class |
absorbance |
A data frame with:
|
pathlength |
A numeric value indicating the pathlength (in cm) of the cuvette used for absorbance measurement. Default is 1 (1cm). |
Details
The inner-filter effect correction procedure is assuming that fluorescence has been measured in 1 cm cuvette. Hence, absorbance will be converted per cm. Note that absorbance spectra should be provided (i.e. not absorption).
Value
An object of class eemlist.
An object of class eem containing:
sample The file name of the eem.
x A matrix with fluorescence values.
em Emission vector of wavelengths.
ex Excitation vector of wavelengths.
Names matching
The names of absorbance variables are expected to match those of the
eems. If the appropriate absorbance spectrum is not found, an uncorrected
eem will be returned and a warning message will be printed.
Sample dilution
Kothawala et al. 2013 have shown that a 2-fold dilution was required for sample presenting total absorbance > 1.5 in a 1 cm cuvette. Accordingly, a message will warn the user if total absorbance is greater than this threshold.
References
Parker, C. a., & Barnes, W. J. (1957). Some experiments with spectrofluorometers and filter fluorimeters. The Analyst, 82(978), 606. doi:10.1039/an9578200606
Kothawala, D. N., Murphy, K. R., Stedmon, C. A., Weyhenmeyer, G. A., & Tranvik, L. J. (2013). Inner filter correction of dissolved organic matter fluorescence. Limnology and Oceanography: Methods, 11(12), 616-630. doi:10.4319/lom.2013.11.616
Examples
library(eemR)
data("absorbance")
folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
eems <- eem_read(folder, import_function = "cary")
eems <- eem_extract(eems, "nano") # Remove the blank sample
# Remove scattering (1st order)
eems <- eem_remove_scattering(eems, "rayleigh")
eems_corrected <- eem_inner_filter_effect(eems, absorbance = absorbance, pathlength = 1)
op <- par(mfrow = c(2, 1))
plot(eems, which = 1)
plot(eems_corrected, which = 1)
par(op)
The names of an eem or eemlist objects
Description
The names of an eem or eemlist objects
Usage
eem_names(eem)
Arguments
eem |
An object of class |
Value
An object of class eemlist.
A character vector containing the names of the EEMs.
Examples
file <- system.file("extdata/cary/", package = "eemR")
eem <- eem_read(file, recursive = TRUE, import_function = "cary")
eem_names(eem)
Set the sample names of an eem or eemlist objects
Description
Set the sample names of an eem or eemlist objects
Usage
eem_names(x) <- value
Arguments
x |
An object of class |
value |
A character vector with new sample names. Must be equal
in length to the number of samples in the |
Value
An eem or eemlist.
Examples
folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
eems <- eem_read(folder, import_function = "cary")
eem_names(eems)
eem_names(eems) <- c("a", "b", "c", "d")
eem_names(eems)
Extract fluorescence peaks
Description
Extract fluorescence peaks
Usage
eem_peaks(eem, ex, em, verbose = TRUE)
Arguments
eem |
An object of class |
ex |
A numeric vector with excitation wavelengths. |
em |
A numeric vector with emission wavelengths. |
verbose |
Logical determining if additional messages should be printed. |
Value
An object of class eemlist.
A data frame containing excitation and emission peak values. See details for more information.
Interpolation
Different excitation and emission wavelengths are often used to measure
EEMs. Hence, it is possible to have mismatchs between measured wavelengths
and wavelengths used to calculate specific metrics. In these
circumstances, EEMs are interpolated using the
interp2 function from the parcma library. A
message warning the user will be prompted if data interpolation is
performed.
See Also
Examples
file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
eem <- eem_read(file, import_function = "cary")
eem_peaks(eem, ex = c(250, 350), em = c(300, 400))
Fluorescence Intensity Calibration Using the Raman Scatter Peak of Water
Description
Normalize fluorescence intensities to the standard scale of Raman Units (R.U).
Usage
eem_raman_normalisation(eem, blank = NA)
Arguments
eem |
An object of class |
blank |
An object of class |
Details
The function will first try to use the provided blank. If the
blank is omitted, the function will then try to extract the blank from the
eemlist object. This is done by looking for sample names containing
one of these complete or partial strings (ignoring case):
nano
miliq
milliq
mq
blank
Note that if blank is omitted, the function will group the
eemlist based on file location and will assumes that there is a
blank sample in each folder. In that context, the blank will be used on
each sample in the same folder. If more than one blank is found they will
be averaged (a message will be printed if this appends).
Consider the following example where there are two folders that could represent scans performed on two different days 'scans_day_1' and 'scans_day_2'.
| scans_day_1 | |
| nano.csv | |
| sample1.csv | |
| sample2.csv | |
| sample3.csv | |
| scans_day_2 | |
| blank.csv | |
| s1.csv | |
| s2.csv | |
| s3.csv | |
In each folder there are three samples and one blank files. In that context, 'eem_remove_blank()' will use the blank 'nano.csv' from 'sample1.csv', 'sample2.csv' and 'sample3.csv'. The same strategy will be used for files in folder 'scans_day_2' but with blank named 'blank.csv'.
Note that the blanks eem are not returned by the function.
The normalization procedure consists in dividing all fluorescence intensities by the area (integral) of the Raman peak. The peak is located at excitation of 350 nm. (ex = 370) between 371 nm. and 428 nm in emission (371 <= em <= 428). Note that the data is interpolated to make sure that fluorescence at em 350 exist.
Value
An object of class eemlist.
An object of class eem containing:
sample The file name of the eem.
x A matrix with fluorescence values.
em Emission vector of wavelengths.
ex Excitation vector of wavelengths.
References
Lawaetz, A. J., & Stedmon, C. A. (2009). Fluorescence Intensity Calibration Using the Raman Scatter Peak of Water. Applied Spectroscopy, 63(8), 936-940.
doi:10.1366/000370209788964548
Murphy, K. R., Stedmon, C. a., Graeber, D., & Bro, R. (2013). Fluorescence spectroscopy and multi-way techniques. PARAFAC. Analytical Methods, 5(23), 6557.
https://pubs.rsc.org/en/content/articlelanding/2013/ay/c3ay41160e
Examples
# Open the fluorescence eem
file <- system.file("extdata/cary/scans_day_1", "sample1.csv", package = "eemR")
eem <- eem_read(file, import_function = "cary")
plot(eem)
# Open the blank eem
file <- system.file("extdata/cary/scans_day_1", "nano.csv", package = "eemR")
blank <- eem_read(file, import_function = "cary")
# Do the normalisation
eem <- eem_raman_normalisation(eem, blank)
plot(eem)
Read excitation-emission fluorescence matrix (eem)
Description
Read excitation-emission fluorescence matrix (eem)
Usage
eem_read(file, recursive = FALSE, import_function)
Arguments
file |
File name or folder containing fluorescence file(s). |
recursive |
logical. Should the listing recurse into directories? |
import_function |
Either a character or a user-defined function to
import a single eem. If a character, it should be one of "cary", "aqualog",
"shimadzu", "fluoromax4". See |
Details
At the moment, Cary Eclipse, Aqualog and Shimadzu EEMs are supported.
eemR will automatically try to determine from which
spectrofluorometer the files originate and load the data accordingly. Note
that EEMs are reshaped so X[1, 1] represents the fluorescence intensity at
X[min(ex), min(em)].
Value
If file is a single filename:
An object of class eem containing:
sample The file name of the eem.
x A matrix with fluorescence values.
em Emission vector of wavelengths.
ex Excitation vector of wavelengths.
If file is a folder, the function returns an object of class
eemlist which is simply a list of eem.
Examples
file <- system.file("extdata/cary/scans_day_1/", package = "eemR")
eems <- eem_read(file, recursive = TRUE, import_function = "cary")
Blank correction
Description
This function is used to remove blank from eems which can help to reduce the effect of scatter bands.
Usage
eem_remove_blank(eem, blank = NA)
Arguments
eem |
An object of class |
blank |
An object of class |
Details
The function will first try to use the provided blank. If the
blank is omitted, the function will then try to extract the blank from the
eemlist object. This is done by looking for sample names containing
one of these complete or partial strings (ignoring case):
nano
miliq
milliq
mq
blank
Note that if blank is omitted, the function will group the
eemlist based on file location and will assumes that there is a
blank sample in each folder. In that context, the blank will be used on
each sample in the same folder. If more than one blank is found they will
be averaged (a message will be printed if this appends).
Consider the following example where there are two folders that could represent scans performed on two different days 'scans_day_1' and 'scans_day_2'.
| scans_day_1 | |
| nano.csv | |
| sample1.csv | |
| sample2.csv | |
| sample3.csv | |
| scans_day_2 | |
| blank.csv | |
| s1.csv | |
| s2.csv | |
| s3.csv | |
In each folder there are three samples and one blank files. In that context, 'eem_remove_blank()' will use the blank 'nano.csv' from 'sample1.csv', 'sample2.csv' and 'sample3.csv'. The same strategy will be used for files in folder 'scans_day_2' but with blank named 'blank.csv'.
Note that the blanks eem are not returned by the function.
Note that blank correction should be performed before Raman
normalization (eem_raman_normalisation()). An error will occur
if trying to perform blank correction after Raman normalization.
Value
An object of class eemlist.
References
Murphy, K. R., Stedmon, C. a., Graeber, D., & Bro, R. (2013). Fluorescence spectroscopy and multi-way techniques. PARAFAC. Analytical Methods, 5(23), 6557. https://pubs.rsc.org/en/content/articlelanding/2013/ay/c3ay41160e
https://pubs.rsc.org/en/content/articlelanding/2013/ay/c3ay41160e
Examples
## Example 1
# Open the fluorescence eem
file <- system.file("extdata/cary/scans_day_1", "sample1.csv", package = "eemR")
eem <- eem_read(file, import_function = "cary")
plot(eem)
# Open the blank eem
file <- system.file("extdata/cary/scans_day_1", "nano.csv", package = "eemR")
blank <- eem_read(file, import_function = "cary")
plot(blank)
# Remove the blank
eem <- eem_remove_blank(eem, blank)
plot(eem)
## Example 2
# Open the fluorescence eem
folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
eems <- eem_read(folder, import_function = "cary")
plot(eems, which = 3)
# Open the blank eem
file <- system.file("extdata/cary/scans_day_1", "nano.csv", package = "eemR")
blank <- eem_read(file, import_function = "cary")
plot(blank)
# Remove the blank
eems <- eem_remove_blank(eems, blank)
plot(eems, which = 3)
# Automatic correction
folder <- system.file("extdata/cary/", package = "eemR")
# Look at the folder structure
list.files(folder, "*.csv", recursive = TRUE)
eems <- eem_read(folder, recursive = TRUE, import_function = "cary")
res <- eem_remove_blank(eems)
Remove Raman and Rayleigh scattering
Description
Remove Raman and Rayleigh scattering
Usage
eem_remove_scattering(eem, type, order = 1, width = 10)
Arguments
eem |
An object of class |
type |
A string, either "raman" or "rayleigh". |
order |
A integer number, either 1 (first order) or 2 (second order). |
width |
Slit width in nm for the cut. Default is 10 nm. |
Value
An object of class eemlist.
References
Lakowicz, J. R. (2006). Principles of Fluorescence Spectroscopy. Boston, MA: Springer US.#'
Murphy, K. R., Stedmon, C. a., Graeber, D., & Bro, R. (2013). Fluorescence spectroscopy and multi-way techniques. PARAFAC. Analytical Methods, 5(23), 6557. https://doi.org/10.1039/c3ay41160e#'
https://pubs.rsc.org/en/content/articlelanding/2013/AY/c3ay41160e
Examples
# Open the fluorescence eem
file <- system.file("extdata/cary/scans_day_1", "sample1.csv", package = "eemR")
eem <- eem_read(file, import_function = "cary")
plot(eem)
# Remove the scattering
eem <- eem_remove_scattering(eem = eem, type = "raman", order = 1, width = 10)
eem <- eem_remove_scattering(eem = eem, type = "rayleigh", order = 1, width = 10)
plot(eem)
Set Excitation and/or Emission wavelengths
Description
This function allows to manually specify either excitation or emission vector of wavelengths in EEMs. This function is mostly used with spectrophotometers such as Shimadzu that do not include excitation wavelengths in fluorescence files.
Usage
eem_set_wavelengths(eem, ex, em)
Arguments
eem |
An object of class |
ex |
A numeric vector of excitation wavelengths. |
em |
A numeric vector of emission wavelengths. |
Value
An object of class eemlist.
Examples
folder <- system.file("extdata/shimadzu", package = "eemR")
eem <- eem_read(folder, import_function = "shimadzu")
eem <- eem_set_wavelengths(eem, ex = seq(230, 450, by = 5))
plot(eem)
Surface plot of eem
Description
Surface plot of eem
Usage
## S3 method for class 'eemlist'
plot(x, which = 1, interactive = FALSE, show_peaks = FALSE, ...)
Arguments
x |
An object of class |
which |
An integer representing the index of eem to be plotted. |
interactive |
If |
show_peaks |
Boolean indicating if Cobble's peaks should be displayed on the surface plot. Default is FALSE. |
... |
Extra arguments for |
Examples
folder <- system.file("extdata/cary/scans_day_1/", package = "eemR")
eem <- eem_read(folder, import_function = "cary")
plot(eem, which = 3)
Display summary of an eemlist object
Description
Display summary of an eemlist object
Usage
## S3 method for class 'eemlist'
print(x, ...)
Arguments
x |
An object of class |
... |
Extra arguments. |
Value
A data frame containing summarized information on EEMs.
- sample
Character. Sample name of the EEM,
- ex_min
Numerical. Minimum excitation wavelength
- ex_max
Numerical. Maximum excitation wavelength
- em_min
Numerical. Minimum emission wavelength
- em_max
Numerical. Maximum emission wavelength
- is_blank_corrected
Logical. TRUE if the sample has been blank corrected.
- is_scatter_corrected
Logical. TRUE if scattering bands have been removed from the sample.
- is_ife_corrected
Logical. TRUE if the sample has been corrected for inner-filter effect.
- is_raman_normalized
Logical. TRUE if the sample has been Raman normalized.
- manufacturer
Character. The name of the manufacturer.
Examples
folder <- system.file("extdata/cary", package = "eemR")
eem <- eem_read(folder, recursive = TRUE, import_function = "cary")
print(eem)
Display summary of an eemlist object
Description
Display summary of an eemlist object
Usage
## S3 method for class 'eemlist'
summary(object, ...)
Arguments
object |
An object of class |
... |
Extra arguments. |
Value
A data frame containing summarized information on EEMs.
- sample
Character. Sample name of the EEM,
- ex_min
Numerical. Minimum excitation wavelength
- ex_max
Numerical. Maximum excitation wavelength
- em_min
Numerical. Minimum emission wavelength
- em_max
Numerical. Maximum emission wavelength
- is_blank_corrected
Logical. TRUE if the sample has been blank corrected.
- is_scatter_corrected
Logical. TRUE if scattering bands have been removed from the sample.
- is_ife_corrected
Logical. TRUE if the sample has been corrected for inner-filter effect.
- is_raman_normalized
Logical. TRUE if the sample has been Raman normalized.
- manufacturer
Character. The name of the manufacturer.
Examples
folder <- system.file("extdata/cary", package = "eemR")
eem <- eem_read(folder, recursive = TRUE, import_function = "cary")
summary(eem)